Our team is participating in igem competition. We're going to use a plasmid with a part of the gene on it that expresses a protein we don't need(GST-tag). We worry that such a protein will affect the product we want to express. I would like to ask whether it is possible to use the method of protein-protein docking to reversely prove that there is no interaction between them and whether the proteins we do not need will affect our pathways. If not, how to prove it? Thanks a lot.
Linhan Hu
Performing Molecular dynamic simulation of both the protein dock complex can justify the hypothesis.
But in the last experimental analysis, Y2H or Immunoprecipitation must be included to support the simulated study.
It is an interesting thing, and in case you want to inversely prove that the two proteins do not interact is difficult. The docking algorithms focus on few parameters like shape, charges, hydrophobicity and then see whether the bound form has lower energy/intact. This way they create multiple different poses and then evaluate them based on physical model and rank them.
You can take any two proteins, and they will interact (theoretically).
Just to prove that 2 proteins do not interact, take multiple known protein pairs that do not interact (for sure) and then dock to see the score/binding affinity. This will give you a population of false-positive.
Take another set and do the same and get the scores for true-positive.
Now, dock your two proteins and see how different the dock score of your interested proteins is? Is it statistically significantly different from True-positive or False-positive? Simple T-test can be used.
From here, you can argue that the proteins do (not) interact. You can do it with two or three different softwires (mostly are available as web server).
Once done, can you please share your finding here. Good luck.
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